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IMA Workshop
Statistical Methods for Gene Expression: Microarrays and Proteomics
September 29-October 3, 2003


Probability and Statistics in Complex Systems: Genomics, Networks, and Financial Engineering, September 1, 2003 - June 30, 2004

Organizers:

Michael A. Newton
Department of Statistics and Department of Biostatistics and Medical Informatics
University of Wisconsin-Madison
newton@stat.wisc.edu
http://www.stat.wisc.edu/~newton/

and

Giovanni Parmigiani
The Sidney Kimmel Comprehensive Cancer Center and Department of Biostatistics
Johns Hopkins University
gp@jhu.edu
http://astor.som.jhmi.edu/~gp

Technological advances and resources created by genome sequencing projects have enabled biomedical scientists to measure precisely and simultaneously the abundance of thousands of molecular targets in living systems. The effect has been dramatic, not only for biology, where now the cellular role for all genes may be investigated, or for medicine, where new drug targets may be found and new approaches discovered for characterizing and treating complex diseases; the effect has also been dramatic for the mathematical and computational sciences. To assess a major component of this activity, the IMA workshop will focus on statistical issues in the study of gene expression both at the level of RNA transcripts and proteomics. Leading investigators will describe current research and future challenges in this area. The workshop format entails three lectures per day and extensive opportunity for fruitful discussion and interaction.

Various microarray technologies for measuring RNA transcript abundance have created some challenging statistical problems. There are many sources of variation in a typical experiment and these can be accounted for using statistical design and analysis-of-variance methodology; but careful attention has to be given to the high-dimensionality and complicated interactions. Statistical methods invoked early in the data analysis pipeline can remove systematic errors and improve subsequent inferences. Robust statistical methods are important to account for influential observations that may be hidden in massive data sets. A wide range of supervised and unsupervised learning methods have been considered to better organize data, be it to infer coordinated patterns of gene expression, to discover molecular signatures of disease subtypes, or to derive various predictions. Related efforts aim to reconstruct regulatory networks from large sets of expression data. Theoretical problems arise in statistical inference when attempting to address thousands of gene-specific hypotheses at once, such as the problem to bound the rate of false detections of differential expression. Further, research in statistical computing concerns infrastructure to enable efficient and flexible calculations with large expression data sets. The workshop will consider these and other pressing problems generated in current research.

WORKSHOP SCHEDULE
Monday Tuesday
MONDAY, SEPTEMBER 29
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30 Coffee and Registration

Reception Room EE/CS 3-176

9:15 Douglas N. Arnold, Scot Adams, and Organizers Welcome and Introduction
9:30 Terry Speed
WEHI, Melbourne and UC Berkeley

Mining a Tandem Mass Spectrometry Database to Determine the Trends and Global Factors Influencing Peptide Fragmentation

Slides:   html    pdf    ps    ppt

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 David Allison
University of Alabama at Birmingham

Applying High-Dimensional Approaches to Microarray Research

Slides:   pdf

11:25
Discussion
11:30 David M. Rocke
University of California, Davis

Measurement Errors and Data Transformation for Gene Expression Data, Proteomics and Metabolomics Data

Slides:   pdf

11:55
Discussion
12:00
Lunch Break
1:30 Atul Butte, MD
Children's Hospital Informatics Program and Harvard Medical School

Integrative Genomics and its Implications for Clinical Research and Care: What Are the Real Issues Beyond Analysis?

Slides:   pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
3:30 Group Photo here  
3:40

IMA Tea and more (with POSTER SESSION)
400 Lind Hall

Shilpi Arora
Princess Margaret Hospital/Ontario Cancer Institute, Toronto
Gene Expression Profiling of Human Oral Cancer Using cDNA Microarrays
Karla Ballman
Mayo Clinic
Fast Loess for Normalizing Microarray Data
Joseph Beyene
University of Toronto
A Spectral Clustering Method for Microarray Data
David B. Dahl
University of Wisconsin - Madison
Modeling Differential Gene Expression using a Dirichlet Process Mixture Model
Shmuel Friedland
IMA
A Theoretical Framework For Reconstructing Missing Data in Genome - Wide Matrix
Rebecka Jornsten
Rutgers University
Data Depth Based Clustering and Classification
Boris Khots/
Dmitriy Khots
Iowa, USA

Why Infinite-dimensional topological groups may work for Genetics data

Slides:   html    pdf    ps    ppt

Pim (W.W.) Kuurman
Animal Sciences Group, Wageningen UR, The Netherlands

Procedure for standardisation and normalisation of cDNA microarrays

Poster file:   pool.pdf
Talk handout:  EAAPpresentatie.pdf
EAAPpresentatie.doc

Wentian Li
The Robert S Boas Center for Genomics and Human Genetics, North Shore LIJ Research Institute
Extreme-Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression
Adriana Lopez
University of Pittsburgh
Cancer tumor classification using gene expression data
Ann L. Oberg
The Mayo Clinic
Joint Estimation of Calibration and Expression for High-density Oligonucleotide Arrays
Lídia Rejtö
University of Delaware
Bayesian Analysis of Microarrays
Hae-Hiang Song
The Catholic University of Korea
Statistical Inference Methods for Detecting Altered Gene Associations
Mahlet G. Tadesse
Texas A&M University
A Bayesian Method for Class Discovery and Gene Selection
Achim Tresch
Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven Germany
Using Text Mining Networks for the Context Specific Interpretation of Expression Data
Kenny Q. Ye
SUNY at Stony Brook
Pooling or not pooling in microarray experiments - an experimental design point of view
Ming Yuan
University of Wisconsin, Madison
Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions
TUESDAY, SEPTEMBER 30
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30 Sandrine Dudoit
University of California, Berkeley

Loss-based estimation methodology with cross-validation: Prediction of clinical outcomes using microarray data

Slides:   pdf

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Hongzhe Li
UC Davis School of Medicine
Microarray Time Course Gene Expresssion Studies: Some Problems and Statistical Methods

Slides:  pdf

11:25
Discussion
11:30 Kathleen Kerr
University of Washington

Empirical Evaluation of Methodologies for Microarray Data Analysis, With Some Thoughts on Statistical Implications

Slides:   pdf

11:55
Discussion
12:00
Lunch Break
1:30 John Quackenbush
The Institute for Genomic Research

Beyond Significance: Integrating Diverse Data Types to Extract Biological Meaning from Microarrays

Slides:   pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
4:00

Soccer match
(weather permitting)

Photo

Van Cleve Park, 15th Ave and Como Ave 
WEDNESDAY, OCTOBER 1
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30 Keith Baggerly
M.D. Anderson Cancer Center

The Analysis of Proteomics Spectra from Serum Samples

Slides:   pdf

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Yee Hwa (Jean) Yang
University of California, San Francisco

Comparing Normalization Methods Based on Splice Array Experiments

Slides:   pdf

11:25
Discussion
11:30 Wolfgang Huber
German Cancer Research Center
Interpretation and Transformation of Microarray Data

Slides:   html    pdf    ps    ppt

11:55
Discussion
12:00
Lunch Break
1:30 Peter J. Munson
DCB, CIT, NIH, DHHS
Mining a Gene Expression Database
2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
3:30 Mississippi walk
(weather permitting)
Begins and ends at EE/CS 3-180
THURSDAY, OCTOBER 2
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30 Geoff McLachlan
University of Queensland

Classification of Microarray Gene-Expression Data

Slides:   html    pdf    ps    ppt

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Christina Kendziorski
University of Wisconsin - Madison

Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions

Slides:    html    pdf    ps    ppt

11:25
Discussion
11:30 Michael Ochs
Fox-Chase Cancer Center

Encoding Prior Biological Knowledge in Functional Genomics Analysis

Slides:   html    pdf    ps    ppt

11:55
Discussion
12:00
Lunch Break
1:30 Marco F. Ramoni
Harvard Medical School

Bayesian Methods for Microarray Data Analysis

Slides:   pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
6:00 Workshop Dinner Jewel of India
1427 Washington Avenue
FRIDAY, OCTOBER 3

NOTE THE ABBREVIATED SCHEDULE FOR FRIDAY; FIRST TALK AT 9:10
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:10 Mark van der Laan
University of California, Berkeley

Prediction of Survival

Slides:   pdf

10:00
Discussion
10:10 Coffee Break Reception Room EE/CS 3-176
10:20 Terry M. Therneau
Mayo Clinic

Joint calibration and fitting of microarray data

Slides:   pdf   ps
Figure:   description    pdf    ps

11:10
Discussion
11:20 Coffee Break Reception Room EE/CS 3-176
11:30 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
11:50
Concluding Remarks by Organizers
12:00
End of Workshop

LIST OF CONFIRMED PARTICIPANTS

NAMEDEPARTMENTAFFILIATION
Edgar AcunaDepartment of Mathematics University of Puerto Rico
Scot AdamsInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Pujya AgarwalLaboratory Medicine and Pathology University of Minnesota, Twin Cities
Soohan AhnDepartment of Statistics Seoul National University
David AllisonDepartment of Biostatistics University of Alabama at Birmingham
Bilgin AltundasInstitute for Mathematics and its Applications Schlumberger-Doll
Greg AndersonSchool of Mathematics University of Minnesota, Twin Cities
Douglas ArnoldInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Donald AronsonInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Shilpi AroraCancer Institute Princess Margaret Hospital
Gerard AwanouInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Mary BaddorfDepartment of Molecular Veterinary Biosciences University of Minnesota, Twin Cities
Keith BaggerlyM. D. Anderson Cancer Center University of Texas, Austin
Karen BallInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Karla BallmanDivision of Biostatistics Mayo Clinic
Antar BandyopadhyayInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Joseph BeyenePopulation Health Sciences Research Institute Hospital for Sick Children
Maury BramsonSchool of Mathematics University of Minnesota, Twin Cities
Olga BrezhnevaInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Michael BrimacombeDepartment of Preventive Medicine New Jersey Medical School of UMDNJ
Philippe Broet Universit√© de Paris XI (Paris-Sud)
Atul Butte Children's Hospital Informatics Program
Enrico Capobianco NONE
Uma ChandranDepartment of Pathology Informatics University of Pittsburgh
Meng ChenDepartment of Statistics University of Wisconsin, Madison
Yidong ChenNational Human Genome Research Institute National Institutes of Health
Laura ChiharaDepartment of Mathematics Carleton College
Timothy ChurchDivision of Environmental and Occupational Health University of Minnesota, Twin Cities
Donald ConnellyLaboratory Medicine and Pathology University of Minnesota, Twin Cities
Yan CuiDepartment of Molecular Sciences University of Tennessee
David DahlDepartment of Statistics and Biostatistics and Medical Information University of Wisconsin, Madison
Deborah DawsonDepartment of Preventive and Community Dentistry/Biostat The University of Iowa
Ann DewittDepartment of Genomics 3M
Christian Domnisoru University of St. Thomas
Shen DongDepartment of Chemical Engineering and Materials Science University of Minnesota, Twin Cities
Sandrine DudoitDivision of Biostatistics University of California, Berkeley
Donald DunbarTarget Discovery Organon Inc.
Anja ForcheDepartment of Genetics, Cell Biology and Development University of Minnesota, Twin Cities
Shmuel FriedlandDepartment of Mathematics, Statistics, and Computer Science University of Illinois, Chicago
Patrick GaffneyDepartment of Medicine University of Minnesota, Twin Cities
Tim GaroniInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Elizabeth GarrettDivision of Oncology Biostatistics Johns Hopkins University
Constantine GatsonisDepartment of Biostatistics Brown University
Balaji GopalakrishnanInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Suzanne GrindleCancer Center, BioInformatics University of Minnesota, Twin Cities
Jennifer HallDepartment of Medicine University of Minnesota, Twin Cities
Chuan-Hsiang HanInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Leonid HaninDepartment of Mathematics Idaho State University
Douglas HawkinsSchool of Statistics University of Minnesota, Twin Cities
Robert HebbelDepartment of Medicine University of Minnesota, Twin Cities
Wolfgang HuberDepartment for Molecular Genome Analysis Deutsches Krebsforschungszentrum (Cancer Research)(DKFZ)
Marianne HuebnerDepartment of Statistics and Probability Michigan State University
Fern HuntMathematical and Computational Sciences Division National Institute of Standards and Technology
Naresh JainSchool of Mathematics University of Minnesota, Twin Cities
Sonia JainDepartment of Biostatistics University of California, San Diego
Yuan JiDepartment of Statistics University of Wisconsin, Madison
Aixiang JiangDepartment of Medicine University of Minnesota, Twin Cities
Kisee JooDepartment of Mathematics University of Kentucky
Rebecka JornstenDepartment of Statistics Rutgers, The State University of New Jersey
Lili JuInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Mahrous KandilDepartment of Soil, Water, and Climate University of Minnesota, Twin Cities
Christina KendziorskiDepartment of Biostatistics and Medical Informatic University of Wisconsin, Madison
Kathleen KerrDepartment of Biostatistics University of Washington
Mohammad KhanDepartment of Mathematics Kent State University
Boris KhotsOil and Gas Division Compressor Controls Corporation
Dohyun KimDepartment of Statistics Seoul National University
Seongjai KimDepartment of Mathematics University of Kentucky
Sek-Won Kong Harvard Medical School
Thomas KurtzDepartment of Mathematics University of Wisconsin, Madison
Pim KuurmanDepartment of Animal Genomics ID-Lelystad
Soumendra LahiriDepartment of Statistics Iowa State University
Jeff LandeMolecular, Cellular and Developmental Biology University of Minnesota, Twin Cities
Taerim LeeDepartment of Information Statistics Seoul National University
Hongzhe LiDepartment of Statistics and Human Genetics University of California, Davis
Wentian LiCenter for Genomics and Human Genetics North Shore - LIJ Research Institute
Chihche Lin University of Minnesota, Twin Cities
Adriana Lopez University of Pittsburgh
Jessica LynchDepartment of Neuroscience University of Minnesota, Twin Cities
Changqing MaCenter for Pathology Informatics University of Pittsburgh
Douglas MahoneyDepartment of Biostatistics Mayo Clinic
Richard McGeheeSchool of Mathematics University of Minnesota, Twin Cities
Geoff McLachlanDepartment of Mathematics University of Queensland
Mario MedvedovicDepartment of Environmental Health University of Cincinnati
Bruce MorlanCancer Center Statistics Mayo Clinic
Peter MunsonMathematical and Statistical Computing Laboratory National Institutes of Health
Haewon NamInstitute of Mathematics and Statistics University of Minnesota, Twin Cities
Michael NewtonDepartment of Statistics University of Wisconsin, Madison
Amir NiknejadDepartment of Mathematics University of Illinois, Chicago
Ann ObergDepartment of Health Science Research Mayo Clinic
Michael OchsBioinformatics Facility Fox Chase Cancer Center
Wei PanDivision of Biostatistics University of Minnesota, Twin Cities
Peter ParkDepartment of Informatics Children's Hospital Boston
Giovanni ParmigianiThe Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University
Lea PopovicInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
John Quackenbush The Institute for Genomic Research
Arvind RaghavanDepartment of Microbiology University of Minnesota, Twin Cities
Marco Ramoni Harvard Medical School
J. RaoDepartment of Biostatistics and Epidemiology Case Western Reserve University
Lidia RejtoDepartment of Food and Recource Economics University of Delaware
Grzegorz RempalaDepartment of Mathematics University of Louisville
David RockeCenter for Image Processing and Integrated Comp. University of California, Davis
Guilherme RosaDepartment of Animal Science Michigan State University
James RosenbergerDepartment of Statistics The Pennsylvania State University
Mauricio SalcedoLaboratorio de Oncologia Genomica Hospital de Oncologia
Fadil SantosaInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Arnd ScheelSchool of Mathematics University of Minnesota, Twin Cities
Paola SebastianiDepartment of Mathematics & Statistics University of Massachusetts
Mark SegalDepartment of Epidemiology and Biostatistics University of San Francisco
Sashirekha ShanmugaveluDepartment of Computer Engineering University of Minnesota, Twin Cities
William ShannonDivision of General Medical Sciences Washington University School of Medicine
Hae-Hiang SongDepartment of Biostatistics The Catholic University of Korea
Terence SpeedDepartment of Statistics University of California, Berkeley
Jingran Sun University of Minnesota, Twin Cities
Mahlet TadesseDepartment of Statistics Texas A & M University
Joachim TheilhaberCambridge Genomics Center Aventis Pharmaceuticals, Inc.
Terry TherneauDivision of Biostatistics Mayo Clinic
Achim TreschDepartment of Bioinformatics Fraunhofer Institute
Mark van der LaanDivision of Biostatistics University of California, Berkeley
Marina VannucciDepartment of Statistics Texas A & M University
Jing WangInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Lin WangDepartment of Microbial Engineering University of Minnesota, Twin Cities
Stephen WillsonDepartment of Mathematics Iowa State University
Fred WrightDepartment of Biostatistics University of North Carolina
Guanghua Xiao University of Minnesota, Twin Cities
Yang Xie University of Minnesota, Twin Cities
Andrei YakovlevCenter for Biostatistics and Computational Biology University of Rochester
Jean YangDivision of Biostatistics University of San Francisco
Yuhong YangDepartment of Statistics Iowa State University
Kenny YeDepartment of Applied Mathematics and Statistics The State University of New York
Haoyu YuDepartment of Supercomputing Institute University of Minnesota, Twin Cities
Ming YuanDepartment of Statistics University of Wisconsin, Madison
Ofer ZeitouniSchool of Mathematics University of Minnesota, Twin Cities
Jun ZhaoInstitute of Mathematics and its Application University of Minnesota, Twin Cities

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